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krgdb_parser.py
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krgdb_parser.py
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import argparse
import os
import re
import requests
import sys
import time
from bs4 import BeautifulSoup
def download_html(rs_id, store=False):
url = f"https://www.ncbi.nlm.nih.gov/snp/{rs_id}"
time.sleep(0.2) # NCBI allows 3 requests per second
try:
response = requests.get(url)
response.raise_for_status()
if store:
with open(f"{rs_id}", 'w', encoding='utf-8') as file:
file.write(response.text)
return response.text
except requests.exceptions.RequestException as e:
print(f"Error fetching {url}: {e}")
return None
# input: "A=0.0007, C=0.0164, T=0.1068"
# return: [('A', '0.0007'), ('C', '0.0164'), ('T', '0.1068')]
def extract_frequency_data(text):
frequency_data = []
parts = text.split(", ")
for part in parts:
allele, freq = part.split("=")
frequency_data.append((allele, freq))
return frequency_data
def parse_html(rs_id, html_doc, output_file=None):
soup = BeautifulSoup(html_doc, 'html.parser')
results = []
position_dt = soup.find('dt', string="Position")
position_dd = position_dt.find_next_sibling('dd')
position_info = position_dd.find('span').text.strip()
grch_version = position_dd.find('span', string=re.compile(r'GRCh')).text.strip()
for tr in soup.find_all('tr'):
a_tags = tr.find_all('a')
for a in a_tags:
if 'KRGDB' in a.text:
tds = tr.find_all('td')
sample_size = ""
frequencies = []
for td in tds:
text = td.text.strip()
if "samp_s" in td.get("class", []):
sample_size = text
elif "=" in text:
frequencies.extend(extract_frequency_data(text))
if frequencies:
ref, ref_freq = frequencies[0]
alts = frequencies[1:]
alt_str = '\t'.join([f"{allele}\t{freq}" for allele, freq in alts])
result_line = f"{rs_id}\t{position_info}\t{grch_version}\t{sample_size}\t{ref}\t{ref_freq}\t{alt_str}"
results.append(result_line)
if not results:
results.append(f"{rs_id}\t{position_info}\t{grch_version}\t0")
if output_file:
with open(output_file, 'a') as file:
file.writelines('\n'.join(results) + '\n')
else:
print('\n'.join(results))
def check_merge(html_content, rs_id):
soup = BeautifulSoup(html_content, 'html.parser')
status_dt = soup.find('dt', string="Status")
if status_dt:
status_dd = status_dt.find_next_sibling('dd')
if status_dd and 'was merged into' in status_dd.text:
new_rs_id_match = re.search(r'href="([^"]+)"', str(status_dd))
if new_rs_id_match:
new_rs_id = new_rs_id_match.group(1).split('/')[-1]
print(f"{rs_id} was merged into {new_rs_id}. Fetching new SNP.")
return new_rs_id
if status_dd and 'Unsupported.' in status_dd.text:
print(f"{rs_id} no longer any supporting observations.")
return 0
return rs_id
def process_single_rs(rs_id, output_file=None, store=False):
if not os.path.exists(rs_id):
html_content = download_html(rs_id, store)
else:
with open(rs_id, 'r', encoding='utf-8') as file:
html_content = file.read()
if html_content:
new_rs = check_merge(html_content, rs_id)
if new_rs == rs_id:
parse_html(rs_id, html_content, output_file)
elif new_rs == 0:
if output_file:
with open(output_file, 'a') as file:
file.writelines(f"{rs_id}\tUnsupported" + '\n')
else:
print(f"{rs_id}\tUnsupported")
else:
process_single_rs(new_rs, output_file, store)
def process_rs_file(input_arg, output_file=None, store=False):
with open(input_arg, 'r', encoding='utf-8') as file:
for rs_id in file:
rs_id = rs_id.strip()
if rs_id:
process_single_rs(rs_id, output_file, store)
def check_output_file_writable(output_file):
if output_file:
try:
with open(output_file, 'a') as file:
pass # Successfully opened for appending, file is writable
except IOError as e:
print(f"Unable to write to output file {output_file}: {e}")
sys.exit(1)
def main():
parser = argparse.ArgumentParser()
parser.add_argument("input_arg", help="input file name or rs ID")
parser.add_argument("-b", "--batch", action="store_true", help="process in batch mode")
parser.add_argument("-o", "--output", help="output file to write results to.", default=None)
parser.add_argument("--store", action="store_true", help="Save fetched HTML content to file named {rs_id}.")
args = parser.parse_args()
check_output_file_writable(args.output)
if args.batch and os.path.exists(args.input_arg):
process_rs_file(args.input_arg, args.output, args.store)
elif re.match(r'^rs\d+$', args.input_arg):
process_single_rs(args.input_arg, args.output, args.store)
else:
print(f"Invalid input or file not found: {args.input_arg}")
if __name__ == "__main__":
main()